The former Episcopal church that once housed the sacrilegious Limelight nightclub will be born again – as a retail mini-mall.

Now known as the Avalon nightclub, the legendary 12,000-square-foot venue on Sixth Avenue at West 20th Street will shutter its doors in early 2007.

“The landlord has decided that he doesn’t want to go forward with another nightclub,” said broker Frank Terzulli, of Winnick Realty Group.

“He’s going to cut it up for retail tenants and a restaurant with patio seating.”

Terzulli added, “The area is becoming more upscale with high-priced condos and stores, and that will make it more difficult to get permits from the community board” for a nightclub.

Cops have been cracking down on Chelsea nightclubs and their rowdy and sometimes violent patrons since the murder last summer of 18-year-old Jennifer Moore, who was killed after a night of drinking at the Guest House nightspot.

Officials have warned club owners that they will conduct more stings on underage drinking and insist that the clubs do more to police themselves.

Community leaders have also complained about Chelsea’s club-filled districts, which have been blasted as a “teenage wasteland.”

Landlord Ben Ashkenazy’s company, Ashkenazy Acquisition Corp., owns and operates several retail malls and the three flagship Barneys stores in New York, Chicago and Beverly Hills.

Sources say international discount-clothing retailer H&M is the likely main tenant for the space, which features triple-height ceilings and mezzanine levels.

A representative for Winnick would not confirm any specific names, since no leases have yet been signed.

Limelight, founded in the deconsecrated church in 1983, hosted some of clubland’s wildest parties in the ’80s and early ’90s under now-deported club king Peter Gatien.

In 1996, federal agents charged that Limelight was a “drug supermarket” and shut it down.

Gatien was acquitted of racketeering and drug charges but convicted of tax evasion. He spent time in jail and was eventually deported to his native Canada.

That same year, one of the club’s flamboyant promoters, Michael Alig, pleaded guilty to manslaughter for killing Angel Melendez, a club regular and reputed drug dealer over a money dispute. He’s still in jail.

Limelight reopened under new management but was shuttered again in 2002.

It came back to life in November of that year as the short-lived Estate. Avalon followed a few months later.